Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012419.1 Corchorus olitorius cultivar O-4 contig12452, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21720
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:493 original size:13 final size:13
Alignment explanation
Indices: 475--502 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
465 TATAGATCTC
475 AAGAGGTGTGTTA
1 AAGAGGTGTGTTA
488 AAGAGGTGTGTTA
1 AAGAGGTGTGTTA
501 AA
1 AA
503 CACCCTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (13 bp):
AAGAGGTGTGTTA
Found at i:4568 original size:26 final size:25
Alignment explanation
Indices: 4539--4591 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
4529 GTACCGTGCT
*
4539 TGCATGGTCTCTTCTTTGTCCTCTTG
1 TGCATGATCTCTTCTTTGTCCT-TTG
*
4565 TGCATGATTTCTTCTTTGTCCTTTG
1 TGCATGATCTCTTCTTTGTCCTTTG
4590 TG
1 TG
4592 TATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.06, C:0.23, G:0.19, T:0.53
Consensus pattern (25 bp):
TGCATGATCTCTTCTTTGTCCTTTG
Found at i:4642 original size:2 final size:2
Alignment explanation
Indices: 4592--4624 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4582 GTCCTTTGTG
4592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4625 CTTGTATACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4751 original size:2 final size:2
Alignment explanation
Indices: 4744--4775 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
4734 CATCATCATC
4744 AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
4776 GTACTAGAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6451 original size:19 final size:19
Alignment explanation
Indices: 6427--6463 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6417 CTTATCTGTA
*
6427 ACCGTTTCACCATCGTTTG
1 ACCGTTTCACCACCGTTTG
6446 ACCGTTTCACCACCGTTT
1 ACCGTTTCACCACCGTTT
6464 TGGCTCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.35, G:0.14, T:0.35
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Found at i:12511 original size:22 final size:22
Alignment explanation
Indices: 12484--12534 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
12474 TTGGCATCGT
* *
12484 TTTCGTTTTCTTTTTTTTTTTG
1 TTTCGTTTTCGTTTTCTTTTTG
12506 TTTCGTTTTCGTTTTCTTTTTG
1 TTTCGTTTTCGTTTTCTTTTTG
*
12528 TTGCGTT
1 TTTCGTT
12535 GTCAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.00, C:0.12, G:0.14, T:0.75
Consensus pattern (22 bp):
TTTCGTTTTCGTTTTCTTTTTG
Found at i:19510 original size:4 final size:4
Alignment explanation
Indices: 19486--19538 Score: 51
Period size: 4 Copynumber: 14.0 Consensus size: 4
19476 TTAAACATAG
* *
19486 CTAA CTAA ATAA CTAA GTAA CTAA CT-A CTAA C-AA -TCAA CTAA CT-A
1 CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CT-AA CTAA CTAA
19531 CTAA CTAA
1 CTAA CTAA
19539 TTAGTATAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
3 8 0.20
4 31 0.77
5 1 0.03
ACGTcount: A:0.51, C:0.23, G:0.02, T:0.25
Consensus pattern (4 bp):
CTAA
Found at i:20002 original size:11 final size:11
Alignment explanation
Indices: 19986--20033 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
19976 GAAGTTCGTG
19986 TTTGAAGACCA
1 TTTGAAGACCA
**
19997 TTTGAAGATAA
1 TTTGAAGACCA
20008 TTTGAAGA-C-
1 TTTGAAGACCA
20017 -TTGAAGACCA
1 TTTGAAGACCA
20027 -TTGAAGA
1 TTTGAAGA
20034 TTTATTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:21434 original size:15 final size:15
Alignment explanation
Indices: 21404--21445 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
21394 TTACTTTGCT
21404 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
21420 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
21435 TTGCTTTCTGT
1 TTGTTTTCTGT
21446 CAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Done.